Its opposition to Syracuse ultimately led to its capture and destruction in 403 BC at the hands of Dionysius the tyrant, after it had supported Athens during that city's disastrous Sicilian expedition. Though the site continued to be inhabited, most activity shifted to neighbouring Tauromenium.
In the Middle Ages, Naxos had lost importance and even lost its name. During the Arabian period, it was called Al Kusus. During the Norman period Kusus became Kisoi and then Schisò. Since the area was widely cultivated with citrus orchards, it came to be known as "Giardini" and was part of the administrative area of Taormina. In 1846 Ferdinand II, King of the two Sicilies transformed it into an independent commune.
The economic development of Giardini Naxos started around 1870 after the opening of the railway Messina-Catania, and changed the small maritime village into one of the best tourist destinations in Sicily.